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Depending on how geeky you are, you could use the Debug section of the Convert dialog (down at the bottom) to nominate a folder where the intermediate files will be generated.
This will let you see the results of each stage in the conversion process, and identify where the weirdness is creeping in.
Usually it's the initial pdf-to-html stage that has problems, but if you can correct the HTML you can load that into Calibre and convert it to MOBI.
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